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Open Access Highly Accessed Research article

A consensus linkage map of the grass carp (Ctenopharyngodon idella) based on microsatellites and SNPs

Jun Hong Xia1, Feng Liu2, Ze Yuan Zhu1, Jianjun Fu2, Jianbin Feng2, Jiale Li23* and Gen Hua Yue13*

Author Affiliations

1 Molecular Population Genetics Group, Temasek Life Sciences Laboratory, National University of Singapore, 117604 Republic of Singapore

2 Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, China

3 Aquaculture Division, E-Institute of Shanghai Universities, Shanghai 201306, China

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BMC Genomics 2010, 11:135  doi:10.1186/1471-2164-11-135

Published: 24 February 2010

Abstract

Background

Grass carp (Ctenopharyngodon idella) belongs to the family Cyprinidae which includes more than 2000 fish species. It is one of the most important freshwater food fish species in world aquaculture. A linkage map is an essential framework for mapping traits of interest and is often the first step towards understanding genome evolution. The aim of this study is to construct a first generation genetic map of grass carp using microsatellites and SNPs to generate a new resource for mapping QTL for economically important traits and to conduct a comparative mapping analysis to shed new insights into the evolution of fish genomes.

Results

We constructed a first generation linkage map of grass carp with a mapping panel containing two F1 families including 192 progenies. Sixteen SNPs in genes and 263 microsatellite markers were mapped to twenty-four linkage groups (LGs). The number of LGs was corresponding to the haploid chromosome number of grass carp. The sex-specific map was 1149.4 and 888.8 cM long in females and males respectively whereas the sex-averaged map spanned 1176.1 cM. The average resolution of the map was 4.2 cM/locus. BLAST searches of sequences of mapped markers of grass carp against the whole genome sequence of zebrafish revealed substantial macrosynteny relationship and extensive colinearity of markers between grass carp and zebrafish.

Conclusions

The linkage map of grass carp presented here is the first linkage map of a food fish species based on co-dominant markers in the family Cyprinidae. This map provides a valuable resource for mapping phenotypic variations and serves as a reference to approach comparative genomics and understand the evolution of fish genomes and could be complementary to grass carp genome sequencing project.